Re: [AMBER] Specifying size of truncated octahedron box manually

From: David Case <>
Date: Wed, 21 Aug 2019 02:33:01 +0000

On Tue, Aug 06, 2019, Bellesis, Andrew G wrote:
>I am trying to set the dimensions of a truncated octahedron box in tleap
>Here is the context of my problem: I am simulating folding and unfolding
>of proteins. When I start with the folded state, I want to make sure that
>my solvent box is big enough to accomodate the resulting unfolded state +
>12 Angstrom clearance. Therefore, to try and find the right box size to
>start with, I solvated a known unfolded structure to obtain the following
>box information:
>> solvateOct x SPCBOX 12.0
>Scaling up box by a factor of 1.177857 to meet diagonal cut criterion
> Solute vdw bounding box: 79.955 83.697 84.429
> Total bounding box for atom centers: 112.697 112.697 112.697
> (box expansion for 'iso' is 4.8%)
> Solvent unit box: 18.774 18.774 18.774
>The number of boxes: x= 7 y= 7 z= 7
> Volume: 734885.482 A^3 (oct)
>I want to take the box defined here and the use it when I solvate the
>smaller folded protein. How do I do this?

As far as I know, there is no easy way to do this in tleap. Packmol
might be a better choice if you want the same size box for various

[Again, others should pitch in if they know how to solve this problem in


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Received on Tue Aug 20 2019 - 20:00:03 PDT
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